As Paxton continues to deliver his xenophobic address, Enterprise's crew and the delegates assembled at Starfleet Command watch the broadcast in horror. Paxton shows an image of a half-Vulcan, half-human child — Trip and T'Pol's baby — as an example of how humanity's genetic pool will be diluted if alien-human relations continue. He notes that for the next 24 hours, he will guarantee safe passage for all aliens leaving the system. If any non-humans remain in the system after the deadline, Paxton will not hesitate to use the verteron array, and he will starts by blowing up Starfleet Command. As the Enterprise crew works furiously to block Paxton's transmission, they suddenly find their ship being targeted by the array. They manage to bid a hasty escape just as Enterprise is about to be destroyed.
At Starfleet Command, Earth dignitary Nathan Samuels is attempting to hold the conference together. Samuels tells Archer that he must destroy the array. Archer, however, is reluctant, especially since Paxton is still holding Trip and T'Pol hostage. He proposes that he take a small team into the mining facility to stop Paxton and Terra Prime. Using a shuttlepod, Archer and his team hitch a ride on the tail of a comet so that they will be able to reach the array undetected. It's rough-going and the shuttlepod appears to be malfunctioning, but they make it to the surface in one piece.
Meanwhile, Paxton has allowed Trip and T'Pol to see their baby. T'Pol deduces that the child is a binary clone created from their DNA. Paxton notes that he acquired the DNA thanks to a Terra Prime spy aboard Enterprise. Paxton then forces Trip to refine the array's targeting system. Trip tries to sabotage it, but he's found out — still, he refuses to help Paxton turn the array into a deadly weapon.
Later, T'Pol confronts Paxton. Using her bio-scanner, she's come to two conclusions. First of all, her daughter is very ill and requires medical attention. Second, Paxton is suffering from Taggart's Syndrome and is using Rigelian gene therapy to treat himself. The very thing that Paxton's so afraid of — alien knowledge — is the only thing keeping him alive.
On Enterprise, Hoshi is in command, prepared to destroy the array if Archer's mission is unsuccessful. Samuels thinks the time has come to fire on the array, but Hoshi holds firm — she has to give Archer more time. For their part, Archer's team has made it into the mining facility and reunited with Trip. The team bursts in to the control room, just as Hoshi's about to open fire on the array. Relieved, Hoshi stands down.
The team attempts to shut down the array, but an explosive fire fight erupts between Paxton's followers and the Enterprise crew. With Trip knocked out and nearly unconscious, it's up to Archer to fight off Paxton and stop the array. Paxton, however, has locked the sequence — Archer can't prevent the array from firing. At the very last minute, Trip regains consciousness and manages to adjust the targeting system. The array fires into the ocean, resulting in nothing more than a harmless cloud of steam.
With Paxton in custody, Enterprise returns to Earth. The actions of Paxton and Terra Prime, however, continue to have consequences. Samuels notes that the groundbreaking interspecies conference is all but over. Additionally, Trip and T'Pol's daughter, who they've named Elizabeth, is dying. Phlox determines that their human and Vulcan DNA are not compatible.
Meanwhile, Mayweather and Reed realize that the malfunctioning shuttlepod they took on the Mars mission was sabotaged. The culprit , a young engineer named Masaro, is the Terra Prime spy onboard Enterprise. Tragically, Masaro kills himself once he's found out.
Later, at Starfleet Command, Samuels asks his fellow delegates to move ahead with the planned interspecies alliance, despite the actions of Terra Prime. As the crew of Enterprise looks on, Archer delivers a rousing speech, urging all of the species in attendance to work together to explore the stars. Soval, the Vulcan ambassador who once disapproved of Archer and Enterprise's mission, is the first to start clapping. Soon, the delegates are on their feet, giving Archer a standing ovation.
Back on Enterprise, Mayweather makes peace with Gannet, who is actually working for Starfleet Intelligence — her mission was to find the real Terra Prime spy on the ship. Ever the gentleman, Mayweather offers to give her a shuttlepod ride home. Meanwhile, T'Pol and Trip mourn the death of their daughter. Trip tells T'Pol that Phlox discovered something: there was a flaw in the cloning techniques Paxton's doctors used. There's no medical reason why a human and a Vulcan wouldn't be able to produce a healthy child . Tearfully, Trip notes that he finds this new information comforting. Obviously moved, T'Pol wordlessly reaches over and grasps his hand.